Preprocessing

Snakemake preprocessing workflow for the Mytilus genome resequencing.

Heavy files are not included to avoid taking uncessary space but the folder architecture is left.

Build the Singularity image

Use Singularity with version 3+.

sudo singularity build container/preprocessing_container.sif container/preprocessing_container.def

Launch part of pipeline locally for example

conda activate snake_env
snakemake --use-singularity --singularity-args "-B ..." \
--use-conda --conda-prefix mamba \
-j {cores} preprocessing

Launch the pipeline on a Slurm cluster

Use the files cluster_ifb_preproc.slurm and cluster_ifb_quality.slurm